We used the atomic force microscope, AFM, as the primary imaging tool, which allows clear, single-molecule visualization of the DNA-IN complexes. We used various DNA lengths (90, 150, 350, 500 and 1000 bps) whose end sequences are identical to those of HIV DNA ends, as substrates. The complex formation efficiency drops dramatically with DNA length below 150bp. The primary product of the reactions is that of two, linear DNA molecules bound to a protein tetramer, and these complexes go on to aggregate by binding among the protein oligomers, forming spider-like structures. Time-course studies of complex formation strongly suggest the reaction pathway: A protein tetramer first binds to a single DNA resulting in conformational changes that strongly promote binding of the second DNA. At this stage we continue our studies by investigating the complex formation using a variety of modified integrase molecules in an effort to enhance complex formation efficiency with shorter DNA (<25bp) and to disrupt the aggregation of such complexes.